therascreen EGFR Pyro Kit

For sequencing-based detection and quantitation of cancer-related gene mutations in the EGFR gene

Compliance with EU IVD Directive 98/79/EC

Comprehensive results in real time

Accurate quantification of mutations in the EGFR gene

Easy interpretation of complex sequence information

The therascreen EGFR Pyro Kit is a molecular detection kit for identification of mutations and deletions in the EGFR gene. The kit contains enzymes, primers, and reagents for amplification of the EGFR gene plus buffers, primers, and reagents for detection and quantification of mutations in real time using Pyrosequencing technology on the PyroMark Q24 System.

The therascreen EGFR Pyro Kit is intended for in vitro diagnostic use.

Linearity of deletion 2235del15.

Linearity of deletion 2235del15 in Exon 19.

Performance

Linearity

Linearity was determined using mixtures of plasmids carrying the wild-type or mutant sequence for the mutations GGC->AGC codon 719, ACG->ATG in codon 790, CTG->CGG in codon 858, and the deletions 2235del15 and 2236del15 in Exon 19 (see figure "Linearity of deletion 2235del15"). The plasmids were mixed in proportions to give four levels of mutation (5, 10, 30, and 50%). Each mixture was analyzed with three different lots of the therascreen EGFR Pyro Kit in three Pyrosequencing runs with three replicates each.

The results were linear within an allowable nonlinearity of 5 % units in the tested range of 5 to 50% mutation level. Similar results were obtained for the mutations GGC->AGC in codon 719, ACG->ATG in codon 790, CTG->CGG in codon 858, and the deletion 2236del15 in Exon 19.

Precision

The precision data allows the determination of the total variability of the assays and was obtained at three different levels by analysis of the above mentioned plasmid mixtures with three replicates each.

Repeatability (intra-assay and inter-batch variability) was calculated based on the data for determination of linearity (three runs on the same day using varying lots of the therascreen EGFR Pyro Kit). Intermediate precision (intra laboratory variability) was determined in three runs within one laboratory on three different days with varying operators, PyroMark Q24 instruments, and lots of the therascreen EGFR Pyro Kit. Reproducibility (inter-laboratory variability) was calculated from two runs each in an internal and external laboratory and using varying lots of the therascreen EGFR Pyro Kit.

Precision estimates are expressed as standard deviation of the measured mutation frequencies in % units. The repeatability, intermediate precision, and reproducibility for the deletion 2235del15 in exon 19 was 0.8–1.2, 0.7–2.9, and 0.7–1.8 % units, respectively, in the measured range of 5 to 50% mutation level. Similar results were obtained for the mutations GGC->AGC in codon 719, ACG->ATG in codon 790, CTG->CGG in codon 858, and the deletion 2236del15 in exon 19.

Precision for the deletion 2235del15 in Exon 19

% mutated plasmid

Repeatability (Mean, SD)

Intermediate precision (Mean, SD)

Reproducibility (Mean, SD)

5

7.7, 0.8

7.4, 0.7

7.4, 0.7

10

14.7, 1.1

14.5, 1.3

14.4, 1.1

30

41.8, 1.2

40.0, 2.0

41.5, 1.7

50

59.4, 1.0

58.2, 2.9

60.7, 1.8

All values are given as % units. SD: standard deviation (n=9). % mutated plasmid based on OD260 measurement.

Principle

The therascreen EGFR Pyro Kit is used for quantitative measurements of mutations in codons 719, 768, 790, 858, and 861, as well as deletions and complex mutations in exon 19 of the human EGFR gene in real time using Pyrosequencing technology on the PyroMark Q24 System. The EGFR gene encodes the epidermal growth factor receptor (EGFR) protein. Mutations in the tyrosine kinase domain of the EGFR gene can enable tumor growth and progression. EGFR mutations are found in approximately 10% of non-small cell lung cancer incidences in the US and 35% in East Asia. Additionally, EGFR mutations are found in 6% of brain tumors.

The following mutations are detected:

Exon 18 (719): G719A, G719C, G719S

Exon 19 (Del): 20 deletions and complex mutations

Exon 20 (768 and 790): S768I, T790M

Exon 21 (858–861): L858R, L861Q, L861R

Additional mutations can be detected and analyzed manually.

Procedure

The kit consists of 4 PCR assays: one for detecting mutations in codon 719 (exon 18), one for detecting mutations in codons 768 and 790 (exon 20), one for detecting mutations in codons 858 to 861 (exon 21), as well as one for detecting deletions in exon 19. The 4 regions are amplified separately by PCR and sequenced through the defined region (see figure "Illustration of the EGFR assay"). The amplicon covering codons 768 and 790 is divided into 2 sequencing reactions. Sequences surrounding the defined positions serve as normalization and reference peaks for quantification and quality assessment of the analysis.

After PCR using primers targeting exons 18, 19, 20, and 21, the amplicons are immobilized on Streptavidin Sepharose High Performance beads. Single-stranded DNA is prepared, and the corresponding sequencing primers anneal to the DNA. The samples are then analyzed on the PyroMark Q24 System using assay setup files and a run setup file.

The therascreen EGFR Pyro Kit enables detection and quantitative measurement of mutations in codons 719, 768, 790, and 858–861, as well as deletions and complex mutations in exon 19 of the human EGFR gene. The kit is intended to be used as an aid to identify cancer patients more likely to benefit from treatment with tyrosine kinase inhibitor therapies.